Session 4: Applications and Future of MetaSUB

“Large-scale Data Modeling, Analysis, and Integration with Personal Health” – Andrew Kasarski, Icahn School of Medicine at Mount Sinai, USA

There has never been more data available that is relevant to personal, population, and public health. Genomic data are cheap to obtain and increasingly abundant. Devices give a surfeit of data about individuals. Electronic Medical Records contain some information about individual’s health and how health systems provide care to their patient populations. Governments, the private sector, and crowdsourced initiatives provide yet more streams of data. Analysis of data within each of these modalities has been fruitful, if occasionally difficult. This talk will cover some successes within these modalities and highlight some opportunities and tricky bits of working across these domains to generate actionable insights.

“Digital Disease Detection” – John Brownstein, Harvard Medical School, USA

Over the past fifteen years, Internet technology has significantly changed the landscape of public health surveillance and epidemic intelligence gathering. Disease and outbreak data is disseminated not only through formal online announcements by government agencies, but also through informal channels such as social networking sites, blogs, chat rooms, Web searches, local news media and crowdsourcing platforms. These data streams have been credited with decreasing the time between an outbreak and formal recognition of an outbreak, allowing for an expedited response to the public health threat. Collectively, these online sources create an image of global public health that is fundamentally different from the one produced by traditional public health surveillance infrastructure. Dr. Brownstein will discuss the current capabilities and future directions in the use of the nontraditional data sources for the purposes of public health surveillance and rapid detection of emerging infectious diseases.

“Engineering the New Built Environment” – Linda Nozick, Cornell University, USA

Accommodating rising populations in urban environments strains infrastructure and can drain natural resources. This talk describes population trends across the globe and illustrates the evolution in engineering design to support the development of increasingly large cities. Finally some thoughts on the interface between engineering built environments and metagenomics are offered.

“Copper Alloys and Microbial Ecosystems” – Harold Michels, Copper Development Association, USA

In laboratory tests, several bacteria including Methicillin-Resistant Staphylococcus aureus (MRSA) were placed on the surfaces of copper alloy samples and were found to quickly die. This was followed by clinical trial, conducted in the ICUs of three hospitals, including Memorial Sloane Kettering Cancer Center. A total of six components were made from copper alloys. The microbial burden found on the components made from copper alloys and standard materials were compare to that found to be reduced by 83% on the copper surfaces. The infection rates of patients in standard rooms were also compared to that of patients in copper rooms. The infection rates for patients in the copper rooms were reduced by 58%, with high degree of statistical significant (p= 0.013). Thus the introduction of a limited number of copper components into the rooms, comprising 7% of the room surface area has the potential to reduce infections and improve patient outcomes. Finally, samples were taken from copper alloy railing and door hardware in Grand Central Terminal, and the reduction in bacteria was not only similar to that observed in laboratory tests and the clinical trail, but also illustrated that copper alloys will display strong efficacy for decades after being put into service.

“Standardized Metadata in the Built Environment” – Lynn Schriml, University of Maryland School of Medicine, USA

Standardizing the description of sampling locations within the built environment promotes the exchange and integration of data across the Microbiology of the Built Environment (BE) program. The MIxS-BE minimal metadata standard has been defined as an extension of the Minimal Metadata Standards for any sequence (MIxS) to enable structured samplemetadata annotation. MIxS is a project of the Genomic Standards Consortium (GSC), an international open-
membership working body of researchers promoting community-driven efforts for the reuse and analysis of contextual metadata describing the collected sample, the environment and/or the host, the sample and sequencing methodologies and technologies. The MIxS-BE standard provides a list of twenty –
six surface, sample and building parameters, including occupancy, temperature and humidity, applicable across studies to enable comparison of data.
The MIxS-BE has been incorporated as a new environmental package into the MIxS annual (2014) release to enable metadata submission to the GenBank and BioSample databases. The MIxS- BE minimal set is being complemented by the development of a MIxS-BE Building & Room comprehensive checklist to describe the breadth of sample metadata terms pertinent to the built environment. The MIxS-BE building and room checklist will provide an extensive vocabulary of building, architectural elements, occupancy, ventilation and environment variables. Each term in the standard is defined and associated with a controlled vocabulary of allowable values and their associated syntax.

“The Undiagnosed Disease Network…Not Just Genetics Anymore” – Catherine Brownstein, Harvard Medical School, USA

The Undiagnosed Diseases Network (UDN), builds on the successes of the Undiagnosed Diseases Program at the National Institutes of Health (NIH UDP). Comprised of a coordinating center, six additional clinical sites, and two sequencing cores, the objectives of the UDN are to: (1) improve the level of diagnosis and care for patients with undiagnosed diseases through the development of common protocols designed by an enlarged community of investigators across the Network; (2) facilitate research into the etiology of undiagnosed diseases, by collecting and sharing standardized, high-quality clinical and laboratory data including genotyping, phenotyping, and environmental exposure data; and (3) create an integrated and collaborative research community across multiple clinical sites, and among laboratory and clinical investigators, to investigate the pathophysiology of these rare diseases and to identify options for patient management. This will be done with a broad focus and understanding that not all undiagnosed diseases are due to genetics.

“Educational Outreach: To Swab is to Teach” – Jeanne Garbarino, Rockefeller University, USA

The presentation of scientific information, theories, and techniques to high school and undergraduate students can often be daunting and overwhelming. However, if framed through relevant entry points and accessible big pictures, taking into consideration a multitude of cultural contexts and experience levels, we can promote a genuine interest in science research in the next generation. By giving students the opportunity to execute, analyze, and interpret experiments and studies of their own design, we not only meet several dimensions of the nationally recognized Next Generation Science Standards (NGSS), but we also provide cross -cutting opportunities that require the integration of both knowledge and practice. Microbiome studies can serve as the ideal platform for providing students with a breadth of scientific experiences that reveal the interrelationship between the natural world and human-created environments. This approach has significant relevancy to students’ lives, particularly for students in urban areas, and can open up a path toward a career in STEM.

“Crowdsourcing: The Art of Engaging Volunteers” – Jeff Zhu and Abby Lyons, Clinical and Translational Science Center, USA

On July 15, 2015, we will be conducting a simultaneous 10 hour longitudinal swabbing of all 468 NYC subway stations. This massive undertaking will require up to 350 volunteers. In this talk, we will discuss how the Weill Cornell Clinical and Translational Science Center is using crowdsourcing techniques to recruit and train these volunteers.